Flow cell humidity sensor system

ABSTRACT

A system for monitoring water concentration in gaseous sample is disclosed. It is readily applicable in the synthesis of biopolymer arrays/microarrays involving the use of water-sensitive reagents. A flow cell is provided in which a capacitance sensor is placed separate from a production or synthesis environment. Sample and dry gas may be provided to the flow cell via conduits and valves or a manifold system. Dry gas, such as N 2 , is used to dry the sensor or simply to maintain it in a dried condition. The same gas may be used to drive an optional venturi pump to draw sample for measurement into the cell from the synthesis environment.

THIS APPLICATION CLAIMS PRIORITY TO COPENDING application Ser. No.10/017,336, FILED Dec. 13, 2001, UNDER 35 U.S.C. 120, THE ENTIRETY OFWHICH IS INCOPORATED HERE IN BY REFERENCE.

FIELD OF THE INVENTION

This invention relates to sensor use, particularly capacitance-typehumidity sensors (i.e., dew point sensors). A system for drying ormaintaining sensor dryness in a flow cell is disclosed. It isadvantageously used in synthesis procedures requiring anhydrous ornear-anhydrous environments.

BACKGROUND OF THE INVENTION

It is often important to maintain low-humidity environments in varioussynthesis or manufacturing processes. For instance, successful in-situsynthesis of biopolymer “biochips” or arrays/micorarrays may require ananhydrous, or substantially humidity-free environment, e.g., where thebiopolymer ligands of the array are “grown” in situ using chemicalsynthesis protocols that produce the ligands through stepwise additionof activated monomers. Water concentrations in such an environmentsometimes need to be as low as 1 PPMv (e.g., in laying-down protein orDNA microarrays).

In order to maintain a production environment in an anhydrous ornear-anydrous state—adjusting conditions or terminating activity ifenvironmental conditions pass beyond acceptible limits—accuratemonitoring is required. Typically, in response to sensor readingsindicating higher humidity levels, the production environment is“blown-out” with dry gas, such as N₂ gas. This purges unwanted moisturefrom the synthesis area.

To maintain extremely low water vapor concentrations, measurements aretypically taken using a capacitance-type sensor. In a capacitance or dewpoint sensor, water vapor absorbed or desorbed by a porous layer altersthe layer's capacitance. This alteration is measured using adjacentconductive members in order to provide a humidity reading.

In such a sensor, water is absorbed much more quickly than it isdesorbed.

Accordingly, it has been appreciated that quicker response time may beachieved in taking humidity measurements using a dry sensor than onethat has already been saturated. A dewpoint meter produced by Xentaur(Medford, NY: Model—XPDM), capitalizes on this feature by isolating asensor in a region filled with dessicant until it is withdrawn therefromand exposed in another region to sample gas.

The present invention, likewise, uses an isolated sensor approach.

However, an improved manner of sensor drying and/or maintaining a sensorin a dry state is taught herein. Instead of requiring a complexapparatus including multiple chambers and perishible dessicants like thereferenced system, a more elegant system is described. In addition tosuch advantages as increased reliability, ease of operation andmaintenance, and cost or space savings, variations of the inventivesystem offer further possible advantages that may be apparent to thoseskilled in the art.

SUMMARY OF THE INVENTION

The present invention includes methods and apparatus for makingminimum-response time water concentration measurements for gas samplesused in various environments with a discrete sample flow cell. Thesample cell includes a capacitance sensor therein. Sample and dry gas,such as N_(2,) is provided to the cell via conduits and valves or amanifold system. The dry gas is used to dry the sensor or simply tomaintain it in a dried condition. The same gas may be used to drive apump, preferably a venturi pump, to draw sample into the sample cell formeasurement.

The inventive system is advantageously used in synthesis proceduresinvolving water-sensitive reactants. Methodology associated therewith,such as the routine for running the flow cell humidity sensor system asparticularly described below, and complete manufacturing systemsincluding printing systems and biological material form part of thepresent invention. Arrays and other products produced using theinventive system may also form part of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

Each of the following figures provide examples diagrammaticallyillustrating aspects of the present invention. Of these,

FIG. 1 shows an overview of the inventive system;

FIG. 2A shows drying flow within a system configuration like that inFIG. 1; and

FIG. 2B shows sampling flow within a system configuration like that inFIG. 1;

FIGS. 3A-3C each show a graphical representation of data characterizingactual performance of a system according to the present invention.

DETAILED DESCRIPTION OF THE INVENTION

Before the present invention is described in detail, it is to beunderstood that this invention is not limited to the particularvariations set forth and may, of course, vary. Various changes may bemade to the invention described and equivalents may be substitutedwithout departing from the true spirit and scope of the invention. Inaddition, many modifications may be made to adapt a particularsituation, material, composition of matter, process, process step orsteps to the objective, spirit and scope of the present invention. Allsuch modifications are intended to be within the scope of the claimsmade herein. Furthermore, where a range of values is provided, it isunderstood that every intervening value, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range is encompassed within the invention. That the upper andlower limits of these smaller ranges may independently be included inthe smaller ranges is also encompassed within the invention, subject toany specifically excluded limit in the stated range. Where the statedrange includes one or both of the limits, ranges excluding either bothof those included limits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can also beused in the practice or testing of the present invention, the preferredmethods and materials are now described. All publications, patents andpatent applications mentioned herein are incorporated herein in theirentirety. The referenced items are provided solely for their disclosureprior to the filing date of the present application. Nothing herein isto be construed as an admission that the present invention is notentitled to antedate such material by virtue of prior invention.

It is also noted that as used herein and in the appended claims, thesingular forms “a,” “and,” and “the” include plural referents unless thecontext clearly dictates otherwise. In the claims, the terms “first,”“second” and so forth are to be interpreted merely as ordinaldesignations, they shall not be limiting in themselves. Further, the useof exclusive terminology such as “solely,” “only” and the like inconnection with the recitation of any claim element is contemplated.Also, it is contemplated that any element indicated to be optionalherein may be specifically excluded from a given claim by way of a“negative” limitation. Finally, it is contemplated that any optionalfeature of the inventive variation(s) described herein may be set forthand claimed independently or in combination with any one or more of thefeatures described herein.

Turning now to FIG. 1, elements of the present invention are shown. Aflow-cell (2) is provided by a body (4) defining a chamber interior (6).The flow cell includes a first port (8) and a second port (10). Otherports as may be convenient can be included as well, so long as theflow-cell (2) and a capacitance type sensor probe (12) located thereincomprise a sealed system when desired, that is discrete or apart fromthe environment from which sample is acquired. A suitable capacitancesensor (12) is produced by Xentaur Corporation (Medford, NY: Model No.XTR-100 or, more preferably, Model No. XTR-100P).

It is preferably operated in a typical fashion, where changes incapacitance across adjacent conductive members is correlated to themoisture content of a gaseous sample by way of appropriatehardware/software, such as an XDT-PM/C transmitting unit availablethrough Xentaur Corporation.

Flow cell body (4) preferably comprises stainless steel. Its interiorwall(s) are preferably electropolished to minimize water adsorptionwithin chamber (6) introduced by sample gas. Chamber (6) is preferablycylindrical. So-shaped, with the first and second ports locatedorthogonally as shown and sensor (12) fixed coaxially, optimal mixing ofgas may be achieved within the chamber around a sensor (12). The size orvolume of the flow cell chamber may be between about 100 to 500 ml. Thedimensions will typically be constrained by mounting the apparatus in aworking environment and ensuring the incoming flow is as homogenous aspossible as it passes over the sensing element.

Lines or conduit members (14) may be used to connect the variouscomponents of the inventive system. However connected, a first valve(16) and a second valve (18) may be provided in fluid communication toflow cell (2). Preferably, the valves are two-way solenoid valves.Suitable valves are produced by KIP Inc. (Farmington, CT: Model No.241043—configured as a two way valve). Together, they serve to open andclose the flow cell, alternately exposing it to sample gas (20) or drygas (22) from a dry gas source or supply (24).

Source (24) may comprise a regulated N₂ tank. Other gasses (especiallyany other dry inert gas or a noble gasses) or source types may be used.What is important is that gas supply (24) be able to deliver anhydrousgas to sensor (12). The purpose of this is to either maintain sensor(12) in a dehydrated state or to provide an environment in which thesensor will desorb water it contains and become dehydrated.

The inventive system may also include a pump (26). The pump preferablycomprises a venturi-type device. Optionally, it is run by dry gas supply(24). Other types of pumps or vacuum devices may be used instead. Forinstance, any common industrial-type vacuum supply may be used. Pump(26) is preferably set to draw sample through flow cell (2) via a siphon(28).

The inventive system may also include third and fourth valves (30) and(32), respectively. These too may be solenoid valves. These valves arepreferably configured for 3-way operation. Suitable valves are producedby KIP Inc. (Farmington, CT: Model No. 241043—configured as a three-wayvalve).

In combination, the hardware thus far described may be used to performvarious tasks. However, as will be apparent, not all of such hardware isnecessary to perform each function. Accordingly, various subcombinationsof the inventive features performing any of the stated functions mayequally be regarded as forming an aspect of the invention as well as acomplete system able to perform all the functions described.

In this regard, it is noted that first and second valves (16) and (18),may be closed-off to isolate flow-cell (2) from high humidity levelsduring servicing of any system plumbing or prolonged delay in use. Thisstate of valve closure defines a “shut-down” mode. In this mode,humidity levels in the flow-cell chamber are maintained substantiallyconstant.

During operation, “dry-down” and “sampling” modes are typicallyemployed. FIG. 2A shows an example of the former, while FIG. 2B shows anexample of the latter.

In dry-down mode, the valves are set so that dry gas is passed throughflow cell (2) by sensor (12). As configured, N₂ gas will also flow outthe venturi pump as exhaust. The desired dry gas flow depicted by adotted path—which is set by valves (16), (18), (30) and (32)—enters flowcell (2) by port (8), passes over and around sensor (12) causing it todesorb moisture and exits flow cell (2) by port (10). Moisture-laden gasmay then exit the inventive system via pump exhaust port (34). Desiredflow rates for such a procedure are between about 0.25 and 2 CFM, set byappropriate pressure.

Running under such conditions, it has been observed that even acompletely saturated sensor (i.e. one registering greater than 1000PPMv) can be adequately dried to a resolution limited steady statemeasurement (i.e. one registering ≦1PPMv) between about 20,000 and30,000 seconds. With an adequately dry sensor (12), upon exposure tomoisture-laden gas an accurate reading may be obtained in about 400seconds. This feature is in comparison to a period of several daysrequired in taking a reading by a sensor simply exposed to sample from atarget environment.

In sampling mode, gas from source (24) running at a higher pressure/flowrate than in dry-down mode is diverted through venturi (26) by valve(32). In FIG. 2B, this activity is again indicated by a dotted path.Flow rates of dry gas to venturi (26) are preferably between about 1 and2 CFM depending on the venturi, driven by pressure set to between about60 and 80 PSI. This generates a vacuum between about 10 and 20 mmHg. Byvirtue of the setup of valves (16), (18) and (30), the vacuum generateddraws sample gas (20) by siphon (28) through flow cell (2) as indicatedin FIG. 2B by dashed lines. Both dry gas and sample gas exit venturiexhaust port (34) as shown.

Using a dry gas/venturi setup is preferred in acquiring sample since italleviates danger of contaminating sensor (12) by hydrated gas thatmight invade the sensor chamber (6) before a steady state is reached.This being said, dry-down and sampling procedures may be accomplishedotherwise. For instance, any sort of vacuum pump may be used to drawsample gas through flow cell (2). Further, dry gas may be passed throughthe flow cell directly without intervening plumbing routing it toachieve multiple functions. Still, the configuration shown in FIG. 1 andthe flow paths shown in FIGS. 2A and 2B comprise most preferred aspectsof the invention.

The inventive system may be set to alternate between sampling anddry-down modes for taking successive humidity readings. In instanceswhere sampling soon after a first sample is taken is not desired orrequired, however, the inventive system may be set to remain in dry-downmode until sensor (12) is sufficiently dry, whereupon flow-cell (2) isisolated by valves (16) and (18) as in the shutdown mode to conserve drygas supplies. Such variability in system usage is preferably implementedwith appropriate electronic hardware under software control. Suitablecontrollers for use in any manner of control of the aforementioned stepsare produced by Keithley Instruments or National Instruments.

In preparation for sampling, a sample siphon end (36) is preferablyplaced in close relation to the target environment that is separate fromflow cell (2). As noted above, the invention is advantageously used inany number of biopolymer array production procedures involving the useof water-sensitive reactants, e.g., activated nucleotides or amino acidsfor the preparation of nucleic acids or polypeptides, respectively. Itmay be most preferred to use features of the invention in connectionwith a protein or DNA array/microarray production environment in whichan ink-jet printhead deposits material onto a substrate. Siphon end (36)is preferably placed within about 1 and 10 mm of the print site or areaction/binding site. The siphon end may be associated with theprinthead to maintain this spacing and move with the printhead tosuccessive sample sites. Alternately, siphon end (36) may remainstationary as long as it is downwind of gas flow within the productionenvironment from the reaction/printing site.

Siphon end (36) is preferably relatively small in order to minimize airdisturbances in the sampling environment. It may have an outer diameterof between about 0.125 and 0.25 inch with an inner diameter betweenabout 0.0625 and 0.125. A typical volume of sample it will obtain may bebetween about 5 liters/minute and 20 liters/minute.

A system advantageously used in connection with the present invention isdescribed in U.S. patent application Ser. No. ______ (attorney docketnumber 10004452, titled “Printhead Fluid Supply System,”) filed on evendate herewith. Further chemical array printing system featuresadvantageously used in connection with the present system are describedin the references cited therein, including U.S. patent application Ser.No. 09/150,504 titled, “Method and Apparatus for Making Nucleic AcidArrays;” U.S. patent application Ser. No. 09/300,589 titled, “Method ofPerforming Array-Based Hybridization Assays Using Thermal InkjetDeposition of Sample Fluids;” U.S. patent application Ser. No.09/846,474 titled “Error Detection In Chemical Array Fabrication”; andU.S. Pat. Nos. 6,242,266 and 6,180,351. Other components of arrayprinting systems which may be adapted for use with the present inventioninclude U.S. Pat. Nos. 4,877,745; 5,338,688; 5,474,796; 5,449,754;5,658,802 and 5,700,637.

Arrays produced with the invention will be used with one or moreadditional components necessary such as sample preparation reagents,buffers, labels or the like. Some or all of these components may beprovided in packaged combination with a set of instructions, possiblyassociated with a package insert or the package itself. Biochip or arraydevices may be used in any number of analyte detection assays includingdifferential gene expression assays, gene identification assays,nucleotide sequencing assays, and the like. Further uses of arrays madeaccording to the present invention are also described in the above citedreferences.

The arrays produced by the subject methods find use in a varietyapplications, where such applications are generally analyte detectionapplications in which the presence of a particular analyte in a givensample is detected at least qualitatively, if not quantitatively.Protocols for carrying out such assays are well known to those of skillin the art and need not be described in great detail here. Generally,the sample suspected of comprising the analyte of interest is contactedwith an array produced according to the subject methods under conditionssufficient for the analyte to bind to its respective binding pair memberthat is present on the array. Thus, if the analyte of interest ispresent in the sample, it binds to the array at the site of itscomplementary binding member and a complex is formed on the arraysurface. The presence of this binding complex on the array surface isthen detected, e.g. through use of a signal production system, e.g. anisotopic or fluorescent label present on the analyte, etc. The presenceof the analyte in the sample is then deduced from the detection ofbinding complexes on the substrate surface.

Specific analyte detection applications of interest includehybridization assays in which the nucleic acid arrays of the subjectinvention are employed. In these assays, a sample of target nucleicacids is first prepared, where preparation may include labeling of thetarget nucleic acids with a label, e.g. a member of signal producingsystem. Following sample preparation, the sample is contacted with thearray under hybridization conditions, whereby complexes are formedbetween target nucleic acids that are complementary to probe sequencesattached to the array surface. The presence of hybridized complexes isthen detected. Specific hybridization assays of interest which may bepracticed using the subject arrays include: gene discovery assays,differential gene expression analysis assays; nucleic acid sequencingassays, and the like. Patents and patent applications describing methodsof using arrays in various applications include: U.S. Pat. Nos.5,143,854; 5,288,644; 5,324,633; 5,432,049; 5,470,710; 5,492,806;5,503,980; 5,510,270; 5,525,464; 5,547,839; 5,580,732; 5,661,028;5,800,992; WO 95/21265; WO 96/31622; WO 97/10365; WO 97/27317; EP 373203; and EP 785 280; the disclosures of which are herein incorporated byreference.

In gene expression analysis with microarrays, an array of “probe”nucleic acids is contacted with a nucleic acid sample of interest.Contact is carried out under hybridization conditions and unboundnucleic acid is then removed. The resultant pattern of hybridizednucleic acid provides information regarding the genetic profile of thesample tested. Gene expression analysis finds use in a variety ofapplications, including: the identification of novel expression ofgenes, the correlation of gene expression to a particular phenotype,screening for disease predisposition, identifying the effect of aparticular agent on cellular gene expression, such as in toxicitytesting; among other applications.

In certain embodiments, the subject methods of analyte detection, asdescribed above, include a step of transmitting data from at least oneof the detecting and deriving steps, as described above, to a remotelocation. The data may be raw data (such as fluorescence intensityreadings for each feature in one or more color channels) or may beprocessed data such as obtained by rejecting a reading for a featurewhich is below a predetermined threshold and/or forming conclusionsbased on the pattern read from the array (such as whether or not aparticular target sequence may have been present in the sample). By“remote location” is meant a location other than the location at whichthe array is present and hybridization occur. For example, a remotelocation could be another location (e.g. office, lab, etc.) in the samecity, another location in a different city, another location in adifferent state, another location in a different country, etc. The datamay be transmitted or otherwise forwarded to the remote location forfurther evaluation and/or use. Any convenient telecommunications meansmay be employed for transmitting the data, e.g., facsimile, modem,internet, etc. When one item is indicated as being “remote” fromanother, this is referenced that the two items are at least in differentbuildings, and may be at least one mile, ten miles, or at least onehundred miles apart. “Communicating” information references transmittingdata representing that information as signals (such as electrical oroptical) over a suitable communication channel (for example, a privateor public network). “Forwarding” an item refers to any means of gettingthat item from one location to the next, whether by physicallytransporting that item or otherwise (where that is possible) andincludes, at least in the case of data, physically transporting a mediumcarrying the data or communicating the data.

Following receipt by a user of an array made by an apparatus or methodof the present invention, as described above, the array will typicallybe exposed to a sample (for example, a fluorescently labeledpolynucleotide or protein containing sample) and the array then read.Reading of the array may be accomplished by illuminating the array andreading the location and intensity of resulting fluorescence at eachfeature of the array. For example, a scanner may be used for thispurpose which is similar to the GENEARRAY scanner manufactured byAgilent Technologies, Palo Alto, Calif. Other suitable apparatus andmethods are described in U.S. patent applications: Ser. No. 09/846125“Reading Multi-Featured Arrays” by Dorsel et al.; and Ser. No. 09/430214“Interrogating Multi-Featured Arrays” by Dorsel et al. However, arraysmay be read by any other method or apparatus than the foregoing, withother reading methods including other optical techniques (for example,detecting chemiluminescent or electroluminescent labels) or electricaltechniques (where each feature is provided with an electrode to detecthybridization at that feature in a manner disclosed in U.S. Pat. No.6,251,685, U.S. Pat. No. 6,221,583 and elsewhere). Results from thereading may be raw results (such as fluorescence intensity readings foreach feature in one or more color channels) or may be processed resultssuch as obtained by rejecting a reading for a feature which is below apredetermined threshold and/or forming conclusions based on the patternread from the array (such as whether or not a particular target sequencemay have been present in the sample, or whether or not a patternindicates a particular condition of an organism from which the samplecame). The results of the reading (processed or not) may be forwarded(such as by communication) to a remote location if desired, and receivedthere for further use (such as further processing).

EXAMPLE

The graphical data shown in FIGS. 3A-3C characterize actual performancewith an embodiment of the present invention. FIG. 3A depicts dry-down ofa capacitance sensor in a flowcell (2) under N₂ purge. The sensorrequires only a matter of hours to reach resolution limited/sub-1 PPMvlevels of H₂O. FIG. 3B depicts sensor (12) response to a step change of6.5 PPMv from house gas reading 0.093 PPMv. The sensor achieves aresolution limited steady state after about 400 seconds. FIG. 3C depictsthe response of an initially dry sensor that has been wetted to greaterthan 12 PPMv and then dried according to the present invention. Theentire process takes roughly 20,000 seconds to achieve a resolutionlimited steady state value.

1-21. (canceled)
 22. An array production system comprising: anenvironment for holding a chemical array substrate, and a capacitancemeasurement system comprising, a body defining a chamber having firstand second ports, said chamber containing a capacitance sensor probe,first and second valves, said first valve in communication with saidfirst port and said second valve in communication with said second port,and a dry gas source, wherein a sampling conduit provides fluidcommunication through said first port between said chamber and saidenvironment, and wherein said valves are positioned to allow dry gas toflow through said chamber in one state to dehydrate said sensor, and agaseous sample from said environment to flow through said chamber inanother state.
 23. The system of claim 22, further comprising a vacuumpump in fluid communication with said chamber to draw sample into saidchamber.
 24. The system of claim 23, wherein said vacuum pump comprisesa venturi device.
 25. The system of claim 24, wherein said venturidevice is driven by said dry gas source.
 26. The system of claim 22,wherein said ports are oriented orthogonally along said body.
 27. Thesystem of claim 22, wherein said first and second valves are two-wayvalves and said system further comprises third and fourth three-wayvalves, said third and fourth valves in communication with each other,said third valve also in communication with said first valve and saidsampling conduit, said fourth valve also in communication with said drygas source and said pump, said second valve also in communication withsaid pump, wherein said pump comprises a venturi device.
 28. A method ofcapacitance measurement for determining water content of a gaseoussample from an environment for holding a chemical array substratecomprising: flowing dry gas over a capacitance sensor provided in a bodydefining a chamber apart from said environment so said sensor desorbswater, terminating said flowing of dry gas, and flowing said gaseoussample from said environment over said sensor to measure water contentof said gaseous sample.
 29. The method of claim 28, further comprisingisolating said capacitance sensor in the presence of dry gas to maintaina low water content.
 30. The method of claim 28, wherein negativepressure from a venturi pump draws said gaseous sample from a samplesite through a flow-cell containing said sensor.
 31. The method of claim28, wherein a biopolymer is synthesized on the substrate in theenvironment.
 32. The method according to claim 31, wherein saidbiopolymer is a polypeptide or nucleic acid.
 33. The method of claim 31,wherein said substrate comprises an array of biomonomers or biopolymersand the substrate is contacted with a fluid provided by the chamber. 34.A capacitance measurement system for determining water content of agaseous sample comprising: a body defining a chamber containing acapacitance sensor probe, a dry gas source, and a venturi device,wherein said system is configured so said venturi device produces anegative pressure within said chamber in one state, wherein said systemis configured so said dry gas source provides a flow of dry gas withinsaid chamber to pass over said sensor probe to dehydrate it in anotherstate, wherein said chamber is apart from an environment for holding anarray substrate, from which environment a gaseous sample is to besampled for moisture by said capacitance sensor probe, and wherein asampling conduit provides fluid communication for said gaseous samplethrough said first port between said chamber and the environment. 35.The system of claim 34, wherein said system is configured to draw saidgaseous sample gas into said chamber by said negative pressure.
 36. Thesystem of claim 34, wherein said venturi device is driven by said drygas.